ObjectiveThe clinical epidemiology of childhood encephalitis in Australia is inadequately understood. We aimed to describe recent trends in childhood encephalitis-related hospitalisation.Study designWe identified encephalitis-related hospital admissions (2000–2012) in national datasets among children ≤14 years using ICD encephalitis codes. We calculated hospitalisation rates and analysed trends by year, age, gender, location, indigenous status and aetiology.ResultsRates of childhood encephalitis hospitalisations significantly declined over an 11-year period (2000–2012; average hospitalisation rate 3.2/100 000). Varicella encephalitis hospitalisations decreased significantly, associated with high levels of varicella vaccine coverage since 2006. Acute disseminated encephalomyelitis (ADEM) was the most common ‘specified’ cause of encephalitis hospitalisation (15%–17%), and its rate has significantly increased. The highest hospitalisation rates occurred in the <1 year age group (5.8/100 000) and varied by location (highest in Northern Territory). The majority (58.9%) of hospitalised encephalitis had no cause identified; this proportion was highest in the <1 year age group (77%). The most common specified infectious causes included: herpes simplex virus, enterovirus, bacterial meningoencephalitis and varicella. When aggregated, the proportion of childhood encephalitis coded as viral was 21.2%.ConclusionHospitalisation of childhood encephalitis has slightly decreased in Australia. High rates of childhood immunisation have been associated with a reduction of varicella-associated encephalitis in Australian children. ADEM, an immune-mediated encephalitis, is the most common recognised cause of encephalitis in children. Young children (<1 year) have the highest admission rates. The high proportion of ‘unspecified’ encephalitis deaths and hospitalisations is an ongoing challenge.